Contacts of the helix formed by residues 91 - 105 (chain D) in PDB entry 1R5V
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 91 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASN* 3.5 40.4 + - - +
88D TRP* 3.1 20.0 + - - +
89D ASN 3.2 2.6 - - - -
90D SER* 1.3 84.7 - - - +
92D PRO* 1.3 68.7 - - - +
93D GLU* 3.1 3.1 - - + -
94D PHE* 2.9 28.1 + - + +
95D LEU* 3.0 11.0 + - - +
14F PHE* 5.5 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASN 4.8 1.0 - - - +
90D SER 3.5 8.9 - - - +
91D GLN* 1.3 86.1 - - - +
93D GLU* 1.3 70.7 + - + +
95D LEU* 3.8 11.2 - - + +
96D GLU* 3.0 26.0 + - - +
99D ARG* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D GLN* 3.1 3.1 - - + -
92D PRO* 1.3 87.4 - - + +
94D PHE* 1.3 62.3 + - - +
96D GLU* 3.5 16.0 + - - +
97D GLN* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D PHE* 4.0 17.7 - + - -
88D TRP* 3.7 45.5 - + + -
91D GLN* 2.9 24.4 + - + +
93D GLU* 1.3 77.8 - - - +
95D LEU* 1.3 66.3 + - - +
97D GLN* 3.0 35.1 + - - +
98D LYS* 3.2 36.5 + - + +
9F LYS* 5.2 4.0 - - + -
10F ALA 5.9 0.2 - - - -
11F ALA* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PHE* 4.2 5.2 - - + -
72D GLY 4.1 14.1 - - - +
73D GLU* 4.2 7.0 - - + +
74D PHE* 3.9 22.4 - - + -
88D TRP 3.9 12.8 - - - +
89D ASN* 3.2 47.8 - - + +
91D GLN 3.0 9.6 + - - +
92D PRO* 3.8 12.1 - - + +
94D PHE* 1.3 77.1 - - + +
96D GLU* 1.3 61.9 + - - +
97D GLN 3.3 0.2 + - - -
98D LYS* 3.3 5.1 + - - +
99D ARG* 3.2 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D PRO 3.0 17.7 + - - +
93D GLU* 3.6 16.2 - - - +
95D LEU* 1.3 76.5 - - - +
97D GLN* 1.3 62.1 + - - +
99D ARG* 3.6 15.5 + - - +
100D ALA* 3.2 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLU 3.4 9.8 + - - +
94D PHE* 3.0 32.2 + - - +
96D GLU* 1.3 78.6 - - - +
98D LYS* 1.3 65.2 + - - +
100D ALA* 3.3 8.4 + - + +
101D GLU* 3.2 29.3 + - + +
104D THR* 4.9 0.3 + - - -
9F LYS* 4.0 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 4.0 7.5 - - + +
55D VAL* 4.6 16.6 - - + -
57D TYR* 4.8 9.2 - - - -
67D PHE* 3.7 31.4 - - + -
74D PHE* 4.2 28.5 - - + -
94D PHE* 3.2 30.7 + - + +
95D LEU* 3.3 6.7 + - - +
97D GLN* 1.3 71.8 - - + +
99D ARG* 1.3 59.5 + - - +
100D ALA 3.0 1.3 - - - -
101D GLU* 2.5 73.0 + - - +
102D VAL* 3.9 1.6 + - - +
8F PRO* 4.1 5.5 - - - +
9F LYS* 3.1 27.5 + - - +
11F ALA* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PHE* 4.1 13.7 - - + -
69D SER* 5.7 4.0 - - - +
72D GLY* 2.7 40.8 + - - +
73D GLU* 4.7 4.9 + - - +
92D PRO 5.8 0.2 + - - -
95D LEU* 3.2 41.9 + - - +
96D GLU* 3.8 11.5 - - - +
97D GLN 3.4 0.2 - - - -
98D LYS* 1.3 77.1 - - - +
100D ALA* 1.3 59.6 + - - +
101D GLU 3.4 0.5 + - - -
102D VAL* 3.5 23.3 + - - +
103D ASP* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLU* 3.2 14.3 + - + +
97D GLN* 3.5 12.8 - - - +
98D LYS 3.0 0.2 - - - -
99D ARG* 1.3 73.4 - - - +
101D GLU* 1.3 58.4 + - - +
102D VAL 3.0 2.9 - - - -
103D ASP* 2.8 14.6 + - - +
104D THR* 2.7 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 3.7 15.9 - - + +
55D VAL* 5.2 0.5 - - - +
97D GLN* 3.2 22.5 + - + +
98D LYS* 2.5 63.3 + - - +
100D ALA* 1.3 72.7 - - - +
102D VAL* 1.3 56.7 + - - +
104D THR* 3.0 13.5 - - - +
105D VAL* 2.7 33.7 + - + +
106D CYS* 3.0 9.7 + - - +
7F TYR 4.4 0.3 - - - +
8F PRO* 3.2 33.0 - - + +
9F LYS* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 3.8 19.5 - - + +
53D LEU* 3.8 15.9 - - + +
69D SER* 3.5 34.3 - - - +
99D ARG 3.5 16.8 + - - +
100D ALA 3.0 0.2 - - - -
101D GLU* 1.3 78.6 - - - +
103D ASP* 1.3 60.5 + - - +
106D CYS* 3.2 12.4 - - - +
107D ARG* 3.1 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG 5.3 0.7 - - - +
100D ALA* 2.8 11.9 + - - +
102D VAL* 1.3 83.2 - - - +
104D THR* 1.3 65.1 + - + +
105D VAL 3.2 1.3 - - - -
107D ARG* 2.8 45.1 + - + +
108D HIS* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLN 4.9 0.3 + - - -
100D ALA* 2.7 30.9 + - + +
101D GLU* 3.0 24.4 + - - +
103D ASP* 1.3 75.1 - - + +
105D VAL* 1.3 61.9 + - - +
108D HIS* 3.2 16.6 - - - +
6F ALA* 3.4 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 5.4 2.2 - - + -
42D CYS* 4.7 8.7 - - - -
53D LEU* 6.2 1.1 - - + -
101D GLU* 2.7 34.8 + - + +
104D THR* 1.3 86.9 - - - +
106D CYS* 1.3 63.7 + - - +
107D ARG 3.7 0.2 - - - -
108D HIS 3.9 0.4 - - - -
109D ASN* 2.8 55.5 + - - +
6F ALA* 3.9 14.6 - - + +
7F TYR 4.1 20.0 - - - +
8F PRO* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il